Evidence map›Paper›PMID 40063808›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.

Doran A Goldman, Katherine S Xue, Autumn B Parrott, Jamie A Lopez, Jean C C Vila, Rashi R Jeeda, Lauryn R Franzese, Rachel L Porter, Ira J Gray, Brian C DeFelice and 4 more

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

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  12. Mixing microbiomes in vitro reveals rules of community assembly.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  13. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Doran A Goldman *Department of Biology, Stanford University, Stanford, CA 94305.ORCID 0009-0001-7838-5209
Katherine S Xue *Department of Biology, Stanford University, Stanford, CA 94305.ORCID 0000-0002-4094-3615
Autumn B ParrottDepartment of Bioengineering, Stanford University, Stanford, CA 94305.
Jamie A LopezDepartment of Bioengineering, Stanford University, Stanford, CA 94305.
Jean C C VilaDepartment of Biology, Stanford University, Stanford, CA 94305.
Rashi R JeedaDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.
Lauryn R FranzeseDepartment of Bioengineering, Stanford University, Stanford, CA 94305.
Rachel L PorterBiophysics Program, Stanford University School of Medicine, Stanford, CA 94305.
Ira J GrayChan Zuckerberg Biohub, San Francisco, CA 94158.
Brian C DeFeliceChan Zuckerberg Biohub, San Francisco, CA 94158.ORCID 0000-0001-8243-0300
Dmitri A PetrovDepartment of Biology, Stanford University, Stanford, CA 94305.
Benjamin H GoodDepartment of Biology, Stanford University, Stanford, CA 94305.ORCID 0000-0002-7757-3347
David A RelmanDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.ORCID 0000-0001-8331-1354
Kerwyn Casey HuangDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.ORCID 0000-0002-8043-8138

Funding

Genomics of rapid adaptation in the lab and in the wildR35GM118165 · NIGMS · STANFORD UNIVERSITY · PI Dmitri Petrov · 2016 to 2026
$8.3M
A universal pipeline for functional characterization of the human microbiota at a massive scaleRM1GM135102 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BUIE, CULLEN RICHARD, DEUTSCHBAUER, ADAM M · 2020 to 2024
$7.6M
Antimicrobial Resistance and Horizontal Gene Transfer in the Human Gut Microbiome in Response to an AntibioticR01AI147023 · NIAID · PALO ALTO VETERANS INSTIT FOR RESEARCH · PI RELMAN, DAVID A. · 2020 to 2024
$3.5M
Quantitative approaches for mapping the real-time evolution of the gut microbiotaR35GM146949 · NIGMS · STANFORD UNIVERSITY · PI Benjamin H Good · 2022 to 2026
$2.0M
Household transmission of the human gut microbiota after antibiotic exposureR21AI168860 · NIAID · STANFORD UNIVERSITY · PI RELMAN, DAVID A. · 2023 to 2024
$426k
NIAID NIH HHS R01 AI147023NIAID NIH HHS R21 AI168860NIGMS NIH HHS R35 GM118165NIGMS NIH HHS R35 GM146949NIGMS NIH HHS RM1 GM135102NIH HHS R01 AI147023
6 · The paper itself

Abstract

The long-term success of introduced populations depends on both their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization dynamics. Here, we investigate how initial population (propagule) size shapes the outcome of community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to neutral ecological theory. Although the composition of the resulting cocultures deviated substantially from neutral expectations, each coculture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. Strain isolates displayed longer-lasting dose dependence when introduced into diverse communities than in pairwise cocultures, consistent with our model's prediction that propagule size should have larger, more persistent effects in diverse communities. Our model also successfully predicted that species with similar resource-utilization profiles, as inferred from growth in spent media and untargeted metabolomics, would show stronger dose dependence in pairwise coculture. This work demonstrates that transient, dose-dependent colonization dynamics can emerge from resource competition and exert long-term effects on the outcomes of community coalescence.

Indexed as

Gastrointestinal MicrobiomeBacteriaCoculture TechniquesEcosystemModels, BiologicalPopulation Densitycompetitionconsumer–resource modelneutral ecological modelniche overlappropagule size

Identifiers

PMID40063808
PMCPMC11929384

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.